Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7qn5
Q-score: 0.58
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- 1,2-dipalmitoyl-sn-glycero-3-phosphate (647 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Nanobody nb25 (13 kDa, Protein from Lama glama)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with nanobody nb25 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (238 Da, Ligand)
- Decane (142 Da, Ligand)
- N-octane (114 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7qn7
Q-score: 0.548
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- 1,2-dipalmitoyl-sn-glycero-3-phosphate (647 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Gamma-amino-butanoic acid (103 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Hexadecane (226 Da, Ligand)
- Decane (142 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- Nanobody nb25 (13 kDa, Protein from Homo sapiens)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with gaba, histamine and nanobody nb25 (Complex from Homo sapiens)
- Water (18 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7qn9
Q-score: 0.505
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Hexadecane (226 Da, Ligand)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with histamine and nanobody nb25 (Complex from Homo sapiens)
- Decane (142 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- Nanobody nb25 (13 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7qnc
Q-score: 0.523
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Nanobody nb25 (13 kDa, Protein from Lama glama)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Human full-length extrasynaptic alpha4beta3delta gaba(a)r in complex with thip (gaboxadol), histamine and nanobody nb25 (Complex from Homo sapiens)
- Gamma-aminobutyric acid receptor subunit alpha-4 (61 kDa, Protein from Homo sapiens)
- Histamine (111 Da, Ligand)
- Decane (142 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit delta (52 kDa, Protein from Homo sapiens)
- 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one (140 Da, Ligand)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7qne
Q-score: 0.606
Sente A, Desai R, Naydenova K, Malinauskas T, Jounaidi Y, Miehling J, Zhou X, Masiulis S, Hardwick SW, Chirgadze DY, Miller KW, Aricescu AR
Nature (2022) 604 pp. 190-194 [ Pubmed: 35355020 DOI: doi:10.1038/s41586-022-04517-3 ]
- Gamma-aminobutyric acid receptor subunit beta-3 (54 kDa, Protein from Homo sapiens)
- Megabody mb38 (13 kDa, Protein from Lama glama)
- [(2r)-2-octanoyloxy-3-[oxidanyl-[(1r,2r,3s,4r,5r,6s)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (746 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{h}-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate (326 Da, Ligand)
- Gaba(a) receptor subunit gamma-2 (56 kDa, Protein from Homo sapiens)
- Decane (142 Da, Ligand)
- N-octane (114 Da, Ligand)
- Gaba(a) receptor subunit alpha-1 (51 kDa, Protein from Homo sapiens)
- Human full-length synaptic alpha1beta3gamma2 gaba(a)r in complex with ro15-4513 and megabody mb38 (Complex from Homo sapiens)
- Chloride ion (35 Da, Ligand)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ldd
Q-score: 0.25
Yu J, Rao P, Clark S, Mitra J, Ha T, Gouaux E
Nature (2021) 594 pp. 448-453 [ DOI: doi:10.1038/s41586-021-03540-0 Pubmed: 33981040 ]
- Glutamate receptor (98 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glua1/a2-symmetric-conformation bound to antibody fragments (Complex)
- Hexadecane (226 Da, Ligand)
- Nonane (128 Da, Ligand)
- 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1h-benzimidazol-2-ol (328 Da, Ligand)
- 15f1 fab light chain (25 kDa, Protein from Mus musculus)
- 11b8 scfv (Complex from Mus musculus)
- Protein cornichon homolog 2 (18 kDa, Protein from Mus musculus)
- N-octane (114 Da, Ligand)
- 11b8 scfv (27 kDa, Protein from Mus musculus)
- 15f1 fab heavy chain (27 kDa, Protein from Mus musculus)
- Glua1/a2-symmetric-conformation (Complex from Mus musculus)
- Decane (142 Da, Ligand)
- Voltage-dependent calcium channel gamma-8 subunit (43 kDa, Protein from Mus musculus)
- Dodecane (170 Da, Ligand)
- Tetradecane (198 Da, Ligand)
- {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2h)-yl]methyl}phosphonic acid (409 Da, Ligand)
- 15f1 fab (Complex from Mus musculus)
- Heptane (100 Da, Ligand)
- Glutamate receptor 1 (101 kDa, Protein from Mus musculus)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7lde
Q-score: 0.221
Yu J, Rao P, Clark S, Mitra J, Ha T, Gouaux E
Nature (2021) 594 pp. 448-453 [ DOI: doi:10.1038/s41586-021-03540-0 Pubmed: 33981040 ]
- Glutamate receptor (98 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hexadecane (226 Da, Ligand)
- Nonane (128 Da, Ligand)
- 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1h-benzimidazol-2-ol (328 Da, Ligand)
- 15f1 fab light chain (25 kDa, Protein from Mus musculus)
- 11b8 scfv (Complex from Mus musculus)
- Glua1/a2-asymmetric-conformation bound to antibody fragments (Complex)
- Protein cornichon homolog 2 (18 kDa, Protein from Mus musculus)
- Glua1/a2-asymmetric-conformation (Complex from Mus musculus)
- N-octane (114 Da, Ligand)
- 11b8 scfv (27 kDa, Protein from Mus musculus)
- 15f1 fab heavy chain (27 kDa, Protein from Mus musculus)
- Decane (142 Da, Ligand)
- Voltage-dependent calcium channel gamma-8 subunit (43 kDa, Protein from Mus musculus)
- Dodecane (170 Da, Ligand)
- Tetradecane (198 Da, Ligand)
- {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2h)-yl]methyl}phosphonic acid (409 Da, Ligand)
- 15f1 fab (Complex from Mus musculus)
- Heptane (100 Da, Ligand)
- Glutamate receptor 1 (101 kDa, Protein from Mus musculus)
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 7lep
Q-score: 0.498
Yu J, Rao P, Clark S, Mitra J, Ha T, Gouaux E
Nature (2021) 594 pp. 448-453 [ DOI: doi:10.1038/s41586-021-03540-0 Pubmed: 33981040 ]
- Tetradecane (198 Da, Ligand)
- {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2h)-yl]methyl}phosphonic acid (409 Da, Ligand)
- Protein cornichon homolog 2 (18 kDa, Protein from Mus musculus)
- Glutamate receptor 2 (47 kDa, Protein from Mus musculus)
- Mix of ampar subunits (glua1, glua3, and glua4) (43 kDa, Protein from Mus musculus)
- Mix of ampar subunits (glua1, glua3, and gluax) (43 kDa, Protein from Mus musculus)
- Composite lbd-tmd complex from the combined hippocampal ampar subtypes (Complex from Mus musculus)
- Dodecane (170 Da, Ligand)
- Decane (142 Da, Ligand)
- Voltage-dependent calcium channel gamma-8 subunit (23 kDa, Protein from Mus musculus)
- 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1h-benzimidazol-2-ol (328 Da, Ligand)
- N-octane (114 Da, Ligand)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Resolution: 1.7 Å
EM Method: Single-particle
Fitted PDBs: 7a5v
Q-score: 0.75
Nakane T, Kotecha A, Sente A, McMullan G, Masiulis S, Brown PMGE, Grigoras IT, Malinauskaite L, Malinauskas T, Miehling J, Uchanski T, Yu L, Karia D, Pechnikova EV, de Jong E, Keizer J, Bischoff M, McCormack J, Tiemeijer P, Hardwick SW, Chirgadze DY, Murshudov G, Aricescu AR, Scheres SHW
Nature (2020) 587 pp. 152-156 [ DOI: doi:10.1038/s41586-020-2829-0 Pubmed: 33087931 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Megabody-25 (Complex from Lama glama)
- Human gaba(a)r-beta3 homopentamer (Complex from Homo sapiens)
- Histamine (111 Da, Ligand)
- Hexadecane (226 Da, Ligand)
- Gamma-aminobutyric acid receptor subunit beta-3,gamma-aminobutyric acid receptor subunit beta-3 (45 kDa, Protein from Homo sapiens)
- Decane (142 Da, Ligand)
- N-octane (114 Da, Ligand)
- Human gaba(a)r-beta3 homopentamer in complex with megabody-25 in lipid nanodisc (485 kDa, Complex)
- Megabody mb25 (56 kDa, Protein from Lama glama)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
afTMEM16 reconstituted in nanodiscs in the presence of Ca2+ and ceramide 24:0
Resolution: 3.59 Å
EM Method: Single-particle
Fitted PDBs: 6e1o
Q-score: 0.471
Falzone ME, Rheinberger J, Lee BC, Peyear T, Sasset L, Raczkowski AM, Eng ET, Di Lorenzo A, Andersen OS, Nimigean CM, Accardi A
eLife (2019) 8 [ Pubmed: 30648972 DOI: doi:10.7554/eLife.43229 ]
- Hexane (86 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Octadecane (254 Da, Ligand)
- Aftmem16 reconstituted in nanodiscs in the presence of ca2+ and ceramide 24:0 (168 MDa, Complex from Aspergillus fumigatus)
- Plasma membrane channel protein (aqy1), putative (84 kDa, Protein from Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
- Decane (142 Da, Ligand)
- Dodecane (170 Da, Ligand)